Extracellular RNA molecules that are pregnancy-specific in maternal plasma have been reported1. They have provided a noninvasive testing tool for fetal assessment and pregnancy monitoring by simply using a peripheral blood specimen from the mother. To date, a number of promising prenatal diagnostic applications have been developed using maternal plasma RNA2-8. Researchers have been actively searching for additional RNA markers in order to extend the applications in different contexts of fetal disorders and pregnancy pathologies.
Theoretically, the most straightforward RNA marker identification method is to directly profile extracellular RNA molecules in maternal plasma. This method has not however been easy because conventional high-throughput screening technologies, such as microarray analysis and serial analysis of gene expression (SAGE), have a limited ability to detect the typically low concentrations of partially degraded extracellular RNA in maternal plasma9. Instead, most of the reported RNA marker screening strategies operate indirectly by comparing the expression profiles of the placenta and the maternal blood cells10. Only the transcripts that are expressed much higher in the placenta than in the maternal blood cells are further studied in maternal plasma samples by high sensitivity but low-throughput technologies, such as real-time reverse transcriptase polymerase chain reaction (RT-PCR). Thus far plasma RNA markers identified by this indirect method are relatively limited. This is possibly because the tissue-based mining strategy has not fully taken into account all of the biological factors influencing placental RNA levels in maternal plasma. In addition, transcripts that are expressed and released by non-placental tissues in response to pregnancy could not be identified by this method. A sensitive and high-throughput methodology that allows the direct profiling of the maternal plasma transcriptome would therefore be very desirable.
Similarly, direct plasma RNA profiling may be useful in other scenarios where there is a mixture of RNA molecules from two individuals, such as for organ transplantation. The circulation of transplantation recipients contains nucleic acid molecules from both the donor and recipient. A change in the relative profile of RNA molecules contributed by the donor or the recipient may reveal pathologies in the transplanted organ or recipient, such as graft rejection.